Mercurial > repos > galaxyp > openms_externalcalibration

comparison ExternalCalibration.xml @ 14:1168fee85066 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:03:40 +0000
parents 61f5ad339398
children 8bdbd9b42f3e
comparison
equal deleted inserted replaced
13:83901afd58c8 14:1168fee85066
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Signal processing and preprocessing]--> 3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
4 <tool id="ExternalCalibration" name="ExternalCalibration" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="ExternalCalibration" name="ExternalCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Applies an external mass recalibration.</description> 5 <description>Applies an external mass recalibration.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">ExternalCalibration</token> 7 <token name="@EXECUTABLE@">ExternalCalibration</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
39 <configfiles> 37 <configfiles>
40 <inputs name="args_json" data_style="paths"/> 38 <inputs name="args_json" data_style="paths"/>
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles> 40 </configfiles>
43 <inputs> 41 <inputs>
44 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input peak file" help=" select mzml data sets(s)"/> 42 <param argument="-in" type="data" format="mzml" optional="false" label="Input peak file" help=" select mzml data sets(s)"/>
45 <param name="offset" argument="-offset" type="float" optional="true" value="0.0" label="Mass offset in ppm" help=""/> 43 <param argument="-offset" type="float" optional="true" value="0.0" label="Mass offset in ppm" help=""/>
46 <param name="slope" argument="-slope" type="float" optional="true" value="0.0" label="Slope (dependent on m/z)" help=""/> 44 <param argument="-slope" type="float" optional="true" value="0.0" label="Slope (dependent on m/z)" help=""/>
47 <param name="power" argument="-power" type="float" optional="true" value="0.0" label="Power (dependent on m/z)" help=""/> 45 <param argument="-power" type="float" optional="true" value="0.0" label="Power (dependent on m/z)" help=""/>
48 <param name="ms_level" argument="-ms_level" type="text" optional="true" value="1 2 3" label="Target MS levels to apply the transformation onto" help="Scans with other levels remain unchanged (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 46 <param argument="-ms_level" type="text" optional="true" value="1 2 3" label="Target MS levels to apply the transformation onto" help="Scans with other levels remain unchanged (space separated list, in order to allow for spaces in list items surround them by single quotes)">
49 <expand macro="list_integer_valsan"/> 47 <expand macro="list_integer_valsan" name="ms_level"/>
50 </param> 48 </param>
51 <expand macro="adv_opts_macro"> 49 <expand macro="adv_opts_macro">
52 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 50 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
53 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 51 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
54 <expand macro="list_string_san"/> 52 <expand macro="list_string_san" name="test"/>
55 </param> 53 </param>
56 </expand> 54 </expand>
57 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 55 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
58 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 56 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
59 </param> 57 </param>
62 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 60 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
63 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 61 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
64 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 62 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
65 </data> 63 </data>
66 </outputs> 64 </outputs>
67 <tests> 65 <tests><!-- TOPP_ExternalCalibration_1_MS1 -->
68 <expand macro="autotest_ExternalCalibration"/> 66 <test expect_num_outputs="2">
69 <expand macro="manutest_ExternalCalibration"/> 67 <section name="adv_opts">
68 <param name="force" value="false"/>
69 <param name="test" value="true"/>
70 </section>
71 <param name="in" value="ExternalCalibration_1_input.mzML"/>
72 <output name="out" file="ExternalCalibration_1_MS1_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
73 <param name="offset" value="-5.5"/>
74 <param name="slope" value="0.0001"/>
75 <param name="power" value="0.0"/>
76 <param name="ms_level" value="1"/>
77 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
78 <output name="ctd_out" ftype="xml">
79 <assert_contents>
80 <is_valid_xml/>
81 </assert_contents>
82 </output>
83 </test>
84 <!-- TOPP_ExternalCalibration_2_MS2 -->
85 <test expect_num_outputs="2">
86 <section name="adv_opts">
87 <param name="force" value="false"/>
88 <param name="test" value="true"/>
89 </section>
90 <param name="in" value="ExternalCalibration_1_input.mzML"/>
91 <output name="out" file="ExternalCalibration_2_MS2_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
92 <param name="offset" value="-5.5"/>
93 <param name="slope" value="0.0001"/>
94 <param name="power" value="0.0"/>
95 <param name="ms_level" value="2"/>
96 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
97 <output name="ctd_out" ftype="xml">
98 <assert_contents>
99 <is_valid_xml/>
100 </assert_contents>
101 </output>
102 </test>
70 </tests> 103 </tests>
71 <help><![CDATA[Applies an external mass recalibration. 104 <help><![CDATA[Applies an external mass recalibration.
72 105
73 106
74 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_ExternalCalibration.html]]></help> 107 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ExternalCalibration.html]]></help>
75 <expand macro="references"/> 108 <expand macro="references"/>
76 </tool> 109 </tool>